10 December 2007

But he that writes of you, if he can tell
That you are you, so dignifies his story,
Let him but copy what in you is writ,
Not making worse what nature made so clear,
And such a counterpart shall fame his wit,
Making his style admired every where.
--Sonnet 84, The Oxford Shakespeare

One of the most common refrains of anti-evolutionists is the claim that evolutionary mechanisms can only degrade what has already come to be. All together now: "No new information!" It's a sad little mantra, an almost religious pronouncement that is made even more annoying by its religious underpinnings, hidden or overt.
But it's a good question: how do new genes come about?

One major source of new genes is gene duplication, which is as conceptually simple as it sounds. It might seem a little odd, and it's not that easy to picture, but the duplication of discrete sections of genetic material is commonplace in genomes. In fact, a significant amount of the genetic variation among individual humans is due to copy number variation, which is variation in the number of copies of particular genes or chunks of genetic material from individual to individual. Genes can be duplicated within a genome via various mechanisms, one of which includes the rare but fascinating occurrence of whole-genome duplication. In any case, it is very clear that gene duplication and subsequent evolution explains the existence of thousands of the most interesting genes in animal genomes.

It should be obvious that gene duplication gives you more genes, but perhaps it's not so clear how this can yield something truly new. For many years, new genes were thought to arise after duplication by a process called neofunctionalization. The basic idea is this: consider a gene A, with a set of functions we'll call F1 and F2. Now suppose the gene is duplicated, so that we now have genes A and B, both capable of carrying out F1 and F2. In neofunctionalization, gene B is free to vary and (potentially) acquire new functions, because gene A is still making sure that F1 and F2 are covered. So the duplication has created an opportunity for a little "experimentation." Most of the time, gene B will be mutated into another piece of genomic debris, a pseudogene with no evident function. (The human genome is riddled with pseudogenes, and that's a story all its own.) Occasionally, though, the tinkering will yield a gene with a new evolutionary trajectory. This model makes good sense and surely accounts for numerous genetic innovations during evolution.

But another model has come to the fore in the last several years, in which the two duplicates seem to "divide and conquer." The process is called subfunctionalization, and the idea is straightforward: gene A covers F1, while gene B covers F2. Straightforward perhaps, but this scenario creates some interesting evolutionary opportunities that aren't immediately obvious. Here in this newest Journal Club, I'll look at another example of the experimental analysis of evolutionary principles and hypotheses, summarizing some recent work that examines subfunctionalization in the laboratory.

In the 11 October issue of Nature, Chris Todd Hittinger and Sean B. Carroll examine an actual example of subfunctionalization in an elegant set of experiments that seeks to re-create the evolutionary changes that occurred after a gene duplication. Specifically, they looked at the events that led to the formation of a new pair of functionally-intertwined genes in yeast. The genes are GAL1 and GAL3, and there are several aspects of this story that make it an ideal system in which to experimentally explore the creation of new genes.

GAL1 and GAL3 arose following a whole-genome duplication in an ancestral yeast species about 100 million years ago. The ancestral form of the gene (see Note 1 at the end of this article) is still present in other species of yeast (namely, those that branched off before the duplication event). This means that the authors were able to compare the new genes (meaning GAL1 and GAL3) and their functions to the single ancestral gene and its functions.

The genomes of these yeast species have been completely decoded, so that the authors had ready access to the sequences of the genes of interest and any DNA sequences in the neighborhood.

Decades of research on yeast have yielded superb tools for the manipulation of the yeast genome. Using these resources, the authors were able to create custom-designed yeast strains in which genes of interest were altered to suit experimental purposes. (Those of us who work in mammalian systems can only dream of being able to do this kind of genetic modification with such ease.)

The biochemical functions of GAL1 and GAL3 were already well known.

Hittinger and Carroll capitalized on this excellent set of tools, and added a key component of their own. They needed a way to measure fitness of different strains of yeast, namely strains that had been modified to resemble various ancestral forms. But most typical methods for testing gene function are unsuitable for estimating fitness, which is the relevant issue. The question, in other words, is focused not on the ability of a particular protein to perform a particular function, but on the ability of a particular protein to change the fitness of the organism that expressed it. The authors' solution can only be described as elegant: they assessed fitness of various yeast strains by measuring the outcomes of head-to-head competitions between strains. Their experimental approach, developed by a colleague (see Note 2) employed some very nice genetic tricks and a sophisticated analytical tool called flow cytometry. (Take some time to read about Abbie Smith's research at ERV if you haven't already done so; in her work on HIV, she asks similar questions regarding fitness and uses a very similar approach in seeking answers.)

Why did the authors choose the GAL1-GAL3 system for close scrutiny? The two genes are critical components of a system in yeast that controls the utilization of galactose (a certain sugar) as an energy source. The GAL1 protein is an enzyme that begins the breakdown of galactose; the GAL3 protein controls the induction of the GAL1 protein. When galactose is present, the GAL3 gene is induced, such that GAL3 protein amounts increase by a few fold. The GAL3 protein is in turn a potent inducer of the GAL1 gene: when galactose is present, GAL1 protein levels increase 1000-fold or so. The two proteins are very similar to each other, and both are very similar to the single protein that is found in the genomes of yeasts that never underwent the genome duplication. So this means that the ancestral protein is bifunctional: it must carry out the very different processes of induction and of galactose metabolism. Not surprisingly, situations like this are thought to involve trade-offs which resolve "adaptive conflicts" between the two different functions of the protein. The reasoning is straightforward: mutations that would improve function A might degrade function B, and vice versa. So the protein is not optimized for either function. There is an adaptive conflict between the two functions. The GAL1-GAL3 system clearly involves subfunctionalization following duplication, and because the ancestral gene is available for comparison, the story invites exploration of the notion of adaptive conflict.

Hittinger and Carroll found that there is indeed an adaptive conflict that was resolved by the evolution of GAL1 and GAL3 following the duplication. But the nature of that conflict is not what some might have predicted. Look again at my description of adaptive conflict above. I focused exclusively on the proteins themselves, claiming that the conflict would arise during attempts to optimize two functions in a single protein. But there's another possibility (that need not exclude the first): perhaps the conflict occurs in the regulation of the expression of those proteins. In the case of GAL1 and GAL3, the two different genes can be turned on and off by two different signaling systems. But in the ancestral situation, there's only one gene and therefore fewer opportunities for diversity in the signaling that leads to expression.

The data presented by Hittinger and Carroll suggest that there is not strong adaptive conflict between the two functions of the ancestral protein. If such a conflict existed, we would expect that changes in GAL1 that make it look more like GAL3 (and vice versa) would cause significant decreases in fitness. But that's not what the fitness analysis showed, and the authors inferred that the adaptive conflict must occur in the arena of regulation, and not in the context of actual protein function. The story is complicated, and I'm not convinced that the authors have ruled out adaptive conflict at the level of the structure of the proteins. Nevertheless, their subsequent experiments demonstrate a clear adaptive conflict in the regulation of expression of the different proteins, and an efficient resolution of that conflict in the subfunctionalization of the two genes following duplication. Those results are strengthened by some detailed structural analysis that seems to account for the physical basis of the optimization that occurred during evolution of the GAL1 and GAL3 genes, optimization that occurred in DNA sequences that control the levels of expression of protein.

If you're a little dizzy at this point, relax and let's zoom out to reflect on this article's significance in evolutionary biology, and its relevance for those who are influenced by the claims of anti-evolution commentators.

First, take note that this article is another example of a sophisticated, hypothesis-driven experimental analysis of a central evolutionary concept. Research like this is reported almost daily, though you'd never learn this by reading the work of Reasons To Believe or the fellows of the Discovery Institute. The mis-characterization of evolutionary biology by the creationists of those organizations is a scandal, and as you might already know, my blog's main purpose is to give evangelical Christians an opportunity to explore the science that is being so carefully avoided by those critics. You don't need to understand sign epistasis or the structure of transcription factors to get this take-home message: evolutionary biologists are hard at work solving the problems that some prominent Christian apologists can't or won't even acknowledge. How does gene duplication lead to the formation of genes with new functions? The folks at the Discovery Institute can't even admit that it happens. Over at Reasons To Believe, they don't mention gene duplication all, despite their fascination with "junk DNA." That's from a ministry that claims to have developed a "testable model" to explain scores of questions regarding origins.

This makes me mad. No matter what you think of the age of the earth or the need for creation miracles, you should be upset by Christians who mangle science to serve apologetic ends.

Second, it's important to note that Hittinger and Carroll's paper is not merely a significant contribution to our understanding of subfunctionalization. It's also a salvo, in an apparently intensifying debate within evolutionary biology regarding the kinds of genetic changes that are more likely to drive evolutionary change. Sean Carroll is one of the leading lights in the new field of evolutionary developmental biology, or evo-devo, and one of the tenets of this upstart school is the claim that most of the genetic changes that lead to adaptation -- and especially to changes in form -- occur in regulatory regions of the genome and not in the genes themselves. (More technically: evo-devo advocates like Carroll postulate that changes in form are more likely to arise from mutations in cis-regulatory regions than in protein-coding sequences within genes.) This assertion is hotly contested, as are many of the other basic views of the evo-devo school. The antagonists include some serious evolutionary biologists, Michael Lynch and Jerry Coyne among them. (Lynch is the guy who took the time to explain why Michael Behe's paper on gene duplication was a joke. Coyne co-wrote the book on speciation, literally.)

I'm a developmental biologist, and therefore partial to many of the arguments of evo-devo thinkers. I'm excited about the union of evolutionary and developmental biology, and I do think that many of the new evo-devo ideas are thought-provoking and potentially fruitful. But the debate is riveting and informative, and I find Lynch and Coyne and their talented colleagues to be alarmingly convincing. I'm worried about some of those cool ideas, but I do take some comfort in this thought: any idea that can survive the onslaught of Lynch and Coyne is a hell of a good idea.

It's easy to see how the disputes spawned by the brash (and perhaps rash) evo-devo folks can lead to innovation and discovery, even if many of their proposals are diminished or destroyed in the process. The disagreement is pretty clear-cut, and both sides seem to agree on how to figure out who's right. They'll go to the lab; they'll perform hypothesis-driven experiments; they'll analyze their data; they'll write up their findings; their work will be subjected to peer review. In other words, they'll do real science.
---Note 1: The ancestral gene itself, of course, isn't available for analysis. The authors are studying the ancestral form of the gene, using a yeast species that never experienced the whole-genome duplication.Note 2: As Hittinger and Carroll indicate in the acknowledgments, the experimental design was developed by Barry L. Williams, who was a postdoctoral fellow in Carroll's lab and is now on the faculty at Michigan State. And by the way, this little state of Michigan doesn't have much of an economy, but boy are we crawling with gifted evolutionary biologists.

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Gene duplication: "Not making worse what nature made so clear"

But he that writes of you, if he can tell
That you are you, so dignifies his story,
Let him but copy what in you is writ,
Not making worse what nature made so clear,
And such a counterpart shall fame his wit,
Making his style admired every where.
--Sonnet 84, The Oxford Shakespeare

One of the most common refrains of anti-evolutionists is the claim that evolutionary mechanisms can only degrade what has already come to be. All together now: "No new information!" It's a sad little mantra, an almost religious pronouncement that is made even more annoying by its religious underpinnings, hidden or overt.
But it's a good question: how do new genes come about?

One major source of new genes is gene duplication, which is as conceptually simple as it sounds. It might seem a little odd, and it's not that easy to picture, but the duplication of discrete sections of genetic material is commonplace in genomes. In fact, a significant amount of the genetic variation among individual humans is due to copy number variation, which is variation in the number of copies of particular genes or chunks of genetic material from individual to individual. Genes can be duplicated within a genome via various mechanisms, one of which includes the rare but fascinating occurrence of whole-genome duplication. In any case, it is very clear that gene duplication and subsequent evolution explains the existence of thousands of the most interesting genes in animal genomes.

It should be obvious that gene duplication gives you more genes, but perhaps it's not so clear how this can yield something truly new. For many years, new genes were thought to arise after duplication by a process called neofunctionalization. The basic idea is this: consider a gene A, with a set of functions we'll call F1 and F2. Now suppose the gene is duplicated, so that we now have genes A and B, both capable of carrying out F1 and F2. In neofunctionalization, gene B is free to vary and (potentially) acquire new functions, because gene A is still making sure that F1 and F2 are covered. So the duplication has created an opportunity for a little "experimentation." Most of the time, gene B will be mutated into another piece of genomic debris, a pseudogene with no evident function. (The human genome is riddled with pseudogenes, and that's a story all its own.) Occasionally, though, the tinkering will yield a gene with a new evolutionary trajectory. This model makes good sense and surely accounts for numerous genetic innovations during evolution.

But another model has come to the fore in the last several years, in which the two duplicates seem to "divide and conquer." The process is called subfunctionalization, and the idea is straightforward: gene A covers F1, while gene B covers F2. Straightforward perhaps, but this scenario creates some interesting evolutionary opportunities that aren't immediately obvious. Here in this newest Journal Club, I'll look at another example of the experimental analysis of evolutionary principles and hypotheses, summarizing some recent work that examines subfunctionalization in the laboratory.

In the 11 October issue of Nature, Chris Todd Hittinger and Sean B. Carroll examine an actual example of subfunctionalization in an elegant set of experiments that seeks to re-create the evolutionary changes that occurred after a gene duplication. Specifically, they looked at the events that led to the formation of a new pair of functionally-intertwined genes in yeast. The genes are GAL1 and GAL3, and there are several aspects of this story that make it an ideal system in which to experimentally explore the creation of new genes.

GAL1 and GAL3 arose following a whole-genome duplication in an ancestral yeast species about 100 million years ago. The ancestral form of the gene (see Note 1 at the end of this article) is still present in other species of yeast (namely, those that branched off before the duplication event). This means that the authors were able to compare the new genes (meaning GAL1 and GAL3) and their functions to the single ancestral gene and its functions.

The genomes of these yeast species have been completely decoded, so that the authors had ready access to the sequences of the genes of interest and any DNA sequences in the neighborhood.

Decades of research on yeast have yielded superb tools for the manipulation of the yeast genome. Using these resources, the authors were able to create custom-designed yeast strains in which genes of interest were altered to suit experimental purposes. (Those of us who work in mammalian systems can only dream of being able to do this kind of genetic modification with such ease.)

The biochemical functions of GAL1 and GAL3 were already well known.

Hittinger and Carroll capitalized on this excellent set of tools, and added a key component of their own. They needed a way to measure fitness of different strains of yeast, namely strains that had been modified to resemble various ancestral forms. But most typical methods for testing gene function are unsuitable for estimating fitness, which is the relevant issue. The question, in other words, is focused not on the ability of a particular protein to perform a particular function, but on the ability of a particular protein to change the fitness of the organism that expressed it. The authors' solution can only be described as elegant: they assessed fitness of various yeast strains by measuring the outcomes of head-to-head competitions between strains. Their experimental approach, developed by a colleague (see Note 2) employed some very nice genetic tricks and a sophisticated analytical tool called flow cytometry. (Take some time to read about Abbie Smith's research at ERV if you haven't already done so; in her work on HIV, she asks similar questions regarding fitness and uses a very similar approach in seeking answers.)

Why did the authors choose the GAL1-GAL3 system for close scrutiny? The two genes are critical components of a system in yeast that controls the utilization of galactose (a certain sugar) as an energy source. The GAL1 protein is an enzyme that begins the breakdown of galactose; the GAL3 protein controls the induction of the GAL1 protein. When galactose is present, the GAL3 gene is induced, such that GAL3 protein amounts increase by a few fold. The GAL3 protein is in turn a potent inducer of the GAL1 gene: when galactose is present, GAL1 protein levels increase 1000-fold or so. The two proteins are very similar to each other, and both are very similar to the single protein that is found in the genomes of yeasts that never underwent the genome duplication. So this means that the ancestral protein is bifunctional: it must carry out the very different processes of induction and of galactose metabolism. Not surprisingly, situations like this are thought to involve trade-offs which resolve "adaptive conflicts" between the two different functions of the protein. The reasoning is straightforward: mutations that would improve function A might degrade function B, and vice versa. So the protein is not optimized for either function. There is an adaptive conflict between the two functions. The GAL1-GAL3 system clearly involves subfunctionalization following duplication, and because the ancestral gene is available for comparison, the story invites exploration of the notion of adaptive conflict.

Hittinger and Carroll found that there is indeed an adaptive conflict that was resolved by the evolution of GAL1 and GAL3 following the duplication. But the nature of that conflict is not what some might have predicted. Look again at my description of adaptive conflict above. I focused exclusively on the proteins themselves, claiming that the conflict would arise during attempts to optimize two functions in a single protein. But there's another possibility (that need not exclude the first): perhaps the conflict occurs in the regulation of the expression of those proteins. In the case of GAL1 and GAL3, the two different genes can be turned on and off by two different signaling systems. But in the ancestral situation, there's only one gene and therefore fewer opportunities for diversity in the signaling that leads to expression.

The data presented by Hittinger and Carroll suggest that there is not strong adaptive conflict between the two functions of the ancestral protein. If such a conflict existed, we would expect that changes in GAL1 that make it look more like GAL3 (and vice versa) would cause significant decreases in fitness. But that's not what the fitness analysis showed, and the authors inferred that the adaptive conflict must occur in the arena of regulation, and not in the context of actual protein function. The story is complicated, and I'm not convinced that the authors have ruled out adaptive conflict at the level of the structure of the proteins. Nevertheless, their subsequent experiments demonstrate a clear adaptive conflict in the regulation of expression of the different proteins, and an efficient resolution of that conflict in the subfunctionalization of the two genes following duplication. Those results are strengthened by some detailed structural analysis that seems to account for the physical basis of the optimization that occurred during evolution of the GAL1 and GAL3 genes, optimization that occurred in DNA sequences that control the levels of expression of protein.

If you're a little dizzy at this point, relax and let's zoom out to reflect on this article's significance in evolutionary biology, and its relevance for those who are influenced by the claims of anti-evolution commentators.

First, take note that this article is another example of a sophisticated, hypothesis-driven experimental analysis of a central evolutionary concept. Research like this is reported almost daily, though you'd never learn this by reading the work of Reasons To Believe or the fellows of the Discovery Institute. The mis-characterization of evolutionary biology by the creationists of those organizations is a scandal, and as you might already know, my blog's main purpose is to give evangelical Christians an opportunity to explore the science that is being so carefully avoided by those critics. You don't need to understand sign epistasis or the structure of transcription factors to get this take-home message: evolutionary biologists are hard at work solving the problems that some prominent Christian apologists can't or won't even acknowledge. How does gene duplication lead to the formation of genes with new functions? The folks at the Discovery Institute can't even admit that it happens. Over at Reasons To Believe, they don't mention gene duplication all, despite their fascination with "junk DNA." That's from a ministry that claims to have developed a "testable model" to explain scores of questions regarding origins.

This makes me mad. No matter what you think of the age of the earth or the need for creation miracles, you should be upset by Christians who mangle science to serve apologetic ends.

Second, it's important to note that Hittinger and Carroll's paper is not merely a significant contribution to our understanding of subfunctionalization. It's also a salvo, in an apparently intensifying debate within evolutionary biology regarding the kinds of genetic changes that are more likely to drive evolutionary change. Sean Carroll is one of the leading lights in the new field of evolutionary developmental biology, or evo-devo, and one of the tenets of this upstart school is the claim that most of the genetic changes that lead to adaptation -- and especially to changes in form -- occur in regulatory regions of the genome and not in the genes themselves. (More technically: evo-devo advocates like Carroll postulate that changes in form are more likely to arise from mutations in cis-regulatory regions than in protein-coding sequences within genes.) This assertion is hotly contested, as are many of the other basic views of the evo-devo school. The antagonists include some serious evolutionary biologists, Michael Lynch and Jerry Coyne among them. (Lynch is the guy who took the time to explain why Michael Behe's paper on gene duplication was a joke. Coyne co-wrote the book on speciation, literally.)

I'm a developmental biologist, and therefore partial to many of the arguments of evo-devo thinkers. I'm excited about the union of evolutionary and developmental biology, and I do think that many of the new evo-devo ideas are thought-provoking and potentially fruitful. But the debate is riveting and informative, and I find Lynch and Coyne and their talented colleagues to be alarmingly convincing. I'm worried about some of those cool ideas, but I do take some comfort in this thought: any idea that can survive the onslaught of Lynch and Coyne is a hell of a good idea.

It's easy to see how the disputes spawned by the brash (and perhaps rash) evo-devo folks can lead to innovation and discovery, even if many of their proposals are diminished or destroyed in the process. The disagreement is pretty clear-cut, and both sides seem to agree on how to figure out who's right. They'll go to the lab; they'll perform hypothesis-driven experiments; they'll analyze their data; they'll write up their findings; their work will be subjected to peer review. In other words, they'll do real science.
---Note 1: The ancestral gene itself, of course, isn't available for analysis. The authors are studying the ancestral form of the gene, using a yeast species that never experienced the whole-genome duplication.Note 2: As Hittinger and Carroll indicate in the acknowledgments, the experimental design was developed by Barry L. Williams, who was a postdoctoral fellow in Carroll's lab and is now on the faculty at Michigan State. And by the way, this little state of Michigan doesn't have much of an economy, but boy are we crawling with gifted evolutionary biologists.